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Well, I took it to an indy down the street(not BMW specific, but seem to know his stuff). He took it for a "spirited" drive(as per my request) and immediately thought it was a rear shock mount.

We got it on the lift, and to our surprise, everything was on point.

The shocks/mounts were fine and the springs are basically brand new (replaced in August 2012).

He poked around, checked for play in the diff(there's a slow leak, checked levels, everything's fine), violently shook the rear wheels... nothing. He popped the trunk, started pressing on **** trying to get the sound to replicate... nothing. He removed the tools from the trunk mounted toolbox and then we went for a drive.

The noise magically disappeared! He thinks it was the tools in the box, I seriously doubt it as the noise was too loud to be that.

Anyways, I'm pretty relieved although very confused. The shop tech only charged me a round of coffees for the visit - pretty cool guy.

Would the noise just stop if the subframe mounts were cracked/torn? I'd think it would be a constant noise.

I've booked an appointment with the subframe specialists(RMP Motorsports) to have my diff oil replaced/flushed. They'll be inspecting the subframe at that point. I'm not quite due for a flush, but I figure $80 for the diff oil change and an inspection is well worth it. They typically charge $50 for the inspection alone.

I'll post updates on Friday after the appointment.

But do you think the noise would disappear, even temporarily, if the subframe was cracked??

Nothing jumped out at him, then again he wasn't a BMW specialist per se. He wasn't too up on the whole subframe ordeal, although he mentioned something abou the "recall"(class action if I'm correct).

Last night before bringing it to him I had removed the following:
Rear lower seat
Spare
Spare cover
Trunk carpeting
Battery Cover + Drivers side organizer/cover
Jack
Probably other things I have forgotten

With all of these items removed, I find it being something rattling in the trunk hard to believe. The noise in the video is quite loud/prominent.

Somebody on another forum said that the suspension being fully unloaded could have caused the rattle to disapear. Maybe a shock was stuck or something, causing the noise. This to me makes sense.

The video, although black, gives you a good indication of when the rattle was apparent. Mostly over bumps, although hard jerky throttle application would cause it too.

After you posted those images(thanks), I crawled under the car and took a look at those mounting points. I didn't see any cracks, and it's definitely not "sunken in" like that last pic - but I didn't have enough room to check all of the angles, as it was very tight under there.

You have to remove the trunk liner and cut through the black rubberized-paper grommet to fully see the condition of the shock mounts. If they're loose or defective, you'll notice.

What springs did your rears get replaced with? If they're not OEM, you can easily have a low-speed clanking noise because they'll bind. The spring pads could be installed incorrectly, off center, or otherwise causing this issue as well.

I somewhat doubt it was the tools though. The battery compartment is also an area where you could have something rattling around.

You have to remove the trunk liner and cut through the black rubberized-paper grommet to fully see the condition of the shock mounts. If they're loose or defective, you'll notice.

What springs did your rears get replaced with? If they're not OEM, you can easily have a low-speed clanking noise because they'll bind. The spring pads could be installed incorrectly, off center, or otherwise causing this issue as well.

I somewhat doubt it was the tools though. The battery compartment is also an area where you could have something rattling around.

The springs are OEM, I guess it's possible they were installed incorrectly - they seemed good to me when we had it on the lift, although I am no expert on suspension.

I already had removed the battery cover, so it couldn't of been that.

I recently stuffed the rear deck with sheets, towels, etc. I'm wondering if that has anything to do with it? Maybe I cracked something by applying too much force when stuffing? I dunno.

The clicking noise was LOUD and constant... I cant see anything that was left inside of the car making that noise. Of course, I could be wrong.